you can ignore the cyl boundary warning.
please do not touch partitions mmcblk2p1, mmcblk2p2, mmcblk2p3, or your reader me become irreversibly bricked.
if you apply sd recovery, your data partition will be flashed with 48mb filesystem, such that the file system has 48mb regardless of the actual partition size...
in order to solve this, you may simply reformat the data partition.
in recovery console, this can be done via
mkfs.ext4 -L data -m 0 -j /dev/mmcblk2p9
missing minitool access may be repaired by re-flashing the enableadb package...